The former Arsenal forward finished a move he started with a thumping finish to break the deadlock before playing a crucial role as Scott Wagstaff put the tie to bed with an accurate finish from outside the penalty area.
With top flight points on their minds Palace, who made 11 changes, never looked like ending their Ashton Gate hoodoo which now stretches back 34 years and 11 visits, even after Owen Garvan's top-draw volley flew in with seconds remaining.
Emmanuel-Thomas' impressive display began before many in the crowd had taken their seats when his powerful effort was hacked off the line just seconds after kick-off and he would then rustle the side-netting after a trademark run.
And the former Ipswich man, reunited with Sean O'Driscoll after a spell together at Doncaster, showed his pace, power and finishing ability when he smashed home the game's opener two minutes before the hour mark.
Despite the introduction of Kevin Phillips, the Premier League side struggled to break down their Sky Bet League One hosts and the game was put to bed with 20 minutes remaining thanks to a smart half-volley from Wagstaff.
In the dying seconds Garvan netted a stunning volley but it was just to be a consolation as Palace's miserable record on this ground continued.